Author

H. Ghodke

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 6 Biochemistry· 3 Bioengineering· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Organism:E. coli· 8 Research Focus:cell signaling & trafficking· 7 Assay:fluorescence / live-cell microscopy· 6 Approach:experimental assay· 5 Approach:microscopy & imaging analysis· 5 Research Focus:chromatin & epigenetic regulation· 2 Assay:DNA methylation· 2 Organism:human· 2

Frequent Co-Authors

A. M. van Oijen· 10 shared S. Jergic· 6 shared N. E. Dixon· 4 shared E. A. Wood· 3 shared H. N. Ho· 3 shared M. M. Cox· 3 shared Z.-Q. Xu· 3 shared A. J. Oakley· 2 shared

Activity by Year

2018-2024 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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10 shared papersBiophysics

A. M. van Oijen

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11 papers

Recent·Most cited

Optimised Nanobody-based Quenchbodies for Enhanced Protein Detection

J. H. Cater, N. Elsalamouny, G. H. Mansour, S. Hutchinson, C. Mc Guinness, S. H. Mueller, R. R. Spinks, N. Shanmugam, A. Pichard-Kostuch, V. Zahoransky, H. Ghodke, M. Ribezzi-Crivellari, H. Yu, A. M. van Oijen, A. D. Griffiths, L. M. Spenkelink

This study optimizes nanobody-based quenchbodies for enhanced protein detection, achieving fluorescence increases of 1.5-2.4-fold and detecting IL-6 down to 2 nM.

bioRxiv · Mar 27, 2024Bioengineering

Structural characterisation of the complete cycle of sliding clamp loading in Escherichia coli

Z.-Q. Xu, S. Jergic, A. T. Y. Lo, A. C. Pradhan, S. H. J. Brown, J. C. Bouwer, H. Ghodke, P. J. Lewis, G. Tolun, A. J. Oakley, N. E. Dixon

This study presents six high-resolution structures of the E. coli clamp loader complex (CLC) during the clamp loading process, revealing the molecular mechanism of clamp opening and DNA binding.

bioRxiv · Jul 20, 2023 · PreprintBiochemistry

Spatiotemporal dynamics of single-stranded DNA intermediates in Escherichia coli

M. E. Cherry, K. Dubiel, C. Henry, E. A. Wood, S. A. Revitt-Mills, J. Keck, M. M. Cox, A. M. van Oijen, H. Ghodke, A. Robinson

The paper uses fluorescence microscopy to study the spatiotemporal dynamics of single-stranded DNA in live E. coli cells, revealing patterns associated with DNA repair and replication.

bioRxiv · May 8, 2023 · PreprintBiophysics

Single-molecule visualization of stalled replication-fork rescue by the Escherichia coli Rep helicase

K. S. Whinn, Z.-Q. Xu, S. Jergic, N. Sharma, L. M. Spenkelink, N. E. Dixon, A. M. van Oijen, H. Ghodke

This study visualizes how the Escherichia coli Rep helicase rescues stalled replication forks by removing roadblocks, showing replication restart is the rate-limiting step.

bioRxiv · Dec 4, 2022 · PreprintBiochemistry

Mechanism of transcription modulation by the transcription-repair coupling factor

B. P. Paudel, Z.-Q. Xu, S. Jergic, A. J. Oakley, N. Sharma, S. H. Brown, J. C. Bouwer, P. Lewis, N. E. Dixon, A. M. van Oijen, H. Ghodke

This study investigates how the bacterial TRCF Mfd modulates transcription by converting elongation complexes into catalytically poised states and then irreversibly terminating transcription through ATP hydrolysis.

bioRxiv · Apr 2, 2021Biophysics

Single-molecule live-cell imaging reveals parallel pathways of prokaryotic nucleotide excision repair

H. Ghodke, H. N. Ho, A. M. van Oijen

The paper uses live-cell imaging to compare UvrA kinetics in TCR-deficient and wild-type E. coli, showing UvrB governs UvrA residence times and UV-induced changes align with Mfd interactions.

Nature Communications · Mar 20, 2020Peer-reviewedBiophysics

Identifying multiple kinetic populations of DNA binding proteins in live cells using single-molecule fluorescence imaging

H. N. Ho, D. Zalami, J. Köhler, A. M. van Oijen, H. Ghodke

This study analyzes the limitations of time-lapse single-molecule fluorescence imaging in measuring kinetic sub-populations of DNA-binding proteins and provides guidelines for reliable data collection and interpretation.

bioRxiv · Jul 25, 2019Biophysics

Modulation of DNA polymerase IV activity by UmuD and RecA* observed by single-molecule time-lapse microscopy

S. S. Henrikus, A. E. McGarth, S. Jergic, M. L. Ritger, P. T. Pham, E. A. Wood, M. F. Goodman, M. M. Cox, A. M. van Oijen, H. Ghodke, A. Robinson

The paper shows UmuD and RecA modulate DNA polymerase IV binding to DNA substrates, with UmuD inhibiting and RecA promoting association, particularly in DNA-damaged cells.

bioRxiv · Jun 23, 2019 · PreprintMicrobiology

Single-molecule imaging reveals molecular coupling between transcription and DNA repair in live cells

H. N. Ho, A. M. van Oijen, H. Ghodke

The paper uses single-molecule imaging to study how transcription and DNA repair interact in live cells, showing that UvrB loading is tightly coupled to Mfd dissociation during repair.

bioRxiv · Jan 8, 2019Biophysics

Nuclease dead Cas9 is a programmable roadblock for DNA replication

K. Whinn, G. Kaur, J. S. Lewis, G. Schauer, S. Müller, S. Jergic, H. Maynard, Z. Yan Gan, M. Naganbabu, M. P. Bruchez, M. O'Donnell, N. E. Dixon, A. M. van Oijen, H. Ghodke

The paper uses a modified Cas9 protein to create a programmable roadblock for studying DNA replication fork arrest in vitro and in vivo.

bioRxiv · Oct 29, 2018Biochemistry

Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response

H. Ghodke, B. Paudel, J. S. Lewis, S. Jergic, K. Gopal, Z. J. Romero, E. A. Wood, R. Woodgate, M. M. Cox, A. M. van Oijen

This study uses a fluorescent probe to track RecA dynamics in live E. coli, showing it is stored during normal metabolism and rapidly mobilizes to form SOS-signaling complexes upon DNA damage.

bioRxiv · Sep 10, 2018Biophysics